I haven't had any experience with my Ram yet but have a highly modified Vette that's been in for warranty work. I have found that if you use your selling dealer, there's less of a chance they'll give you grief... . after all, you just spent 40+k with them. Also, know what's wrong with your rig before you take it in. While not always possible, it allows you to "steer" them in a certain direction and more importantly, shows them that you can't be BS'd if you know what you're talking about. I've yet to have a dealer refuse warranty work because of mods but if a mod of mine "legitimately" causes a problem, I'll suck it up and pay for the work, but if a dealer refuses coverage on my stereo because I have an exhaust system, I'll become the customer from hell really fast. Lastly, if you have a box, and run it conservatively and care for your truck, problems are unlikely as these engines are very "over-built". If you race it around routinely, you're asking for something to go wrong.
When it comes to performance boxes, warranty concerns are one reason that I prefer downloaders... . No non-factory components added to the vehicle that can fail... . Nothing to remove if something goes wrong. You're simply changing parameters in a factory device, that has been designed to allow parameter changes but as I said earlier if your parameter changes causes a problem... you'll be fixing it yourself.